1. Editing with non-elastic tab stops? While Nick's idea is good, the
number of editors that support it is small. Editors are a religious issue.
I doubt that people will switch editors in order to use MMD tables.
2. I would like to see an option for a non-white character. I've been
burned a few times by text processors that convert tabs to spaces. This
will also ease the transition if you are changing the spec.
3. For row spanning, the simplest syntax that is intuitive to me would be a
cell that has a single double-quote character. Effectively saying 'same as
above'.
4. Tables are one of the biggest reasons for using MMD. The ratio of tag
bytes to content bytes can be well over 1. Matching tags is always a pain.
Even the clunkiest syntax proposed on this list has more merit than html
table tags.

My take: It aint broke. Resist fixing it.

1. Continue to support the pipe and multiple pipe syntax. Cells that span
more than 3 columns are very rare, and many of these may be done with a
title instead, or be broken into multiple tables that are floated inline.